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Do queens move away from the brood nest when they shut down?

I've got a few queens left in nucs and wanted to requeen some hives. I went through a dozen hives and couldn't find a single queen. Normally I don't have a problem. About half the time I find the queen on the first pass.

The queens have all shut down, only a scattering of sealed brood. No eggs or open larvae.

So, I'm wondering, do the queens move to another part of the hive after they shut down? I only went through the bottom box. In most cases the second box was plugged out. Could they have moved up into the honey area?